To assess the basis set dependence of different population analysis methods, a comparison of spin populations for five open-shell systems (CF2CCH; C3H7; CH2OH, alpha-4-dehydrotoluene, and a binuclear Cu complex) was carried out across 13 standard basis sets, including minimal basis and variations of the Pople and correlation consistent families of basis sets. Mulliken, Lowdin, Bader's Atoms in Molecules (AIM), Natural Population Analysis (NPA), Hirshfeld, and Minimum Basis Set Mulliken (MBS) are used. In contrast to the well known basis set sensitivity of the Mulliken population, we show that although the spin populations can be somewhat different, the MBS and the NPA methods trend the least with basis set choice. (C) 2010 Elsevier B.V. All rights reserved.